Most of the file is not changed from some sensible default anyway, so we
can store this in the template directory and have a much more manageable
local file which just contains the relevant changes.
The Doxyfile is still in the root directory because this is more like
a configuration file, and also its presence will be a cue to some
users that Doxygen is possible to run on the project.
The directory must be specified with full path to refer to the source
directory. The images will not be referred to by this path, but rather
copied to the output directory (as of Doxygen 1.7.6.1 at least), unlike
the stylesheet (consistency is so last decade).
